/
readgroups_bam_to_readgroups_fastq_lists.cwl
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/
readgroups_bam_to_readgroups_fastq_lists.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/readgroup.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
- id: readgroups_bam_file
type: ../../tools/readgroup.yml#readgroups_bam_file
outputs:
- id: pe_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_pe_file
outputSource: readgroup_fastq_pe/output
- id: se_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_se_file
outputSource: readgroup_fastq_se/output
- id: o1_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_se_file
outputSource: readgroup_fastq_o1/output
- id: o2_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_se_file
outputSource: readgroup_fastq_o2/output
steps:
- id: biobambam_bamtofastq
run: ../../tools/biobambam2_bamtofastq.cwl
in:
- id: filename
source: readgroups_bam_file
valueFrom: $(self.bam)
out:
- id: output_fastq1
- id: output_fastq2
- id: output_fastq_o1
- id: output_fastq_o2
- id: output_fastq_s
- id: bam_readgroup_to_json
run: ../../tools/bam_readgroup_to_json.cwl
in:
- id: INPUT
source: readgroups_bam_file
valueFrom: $(self.bam)
- id: MODE
valueFrom: "lenient"
out:
- id: OUTPUT
- id: decider_readgroup_pe
run: ../../tools/decider_readgroup_expression.cwl
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq1
- id: readgroup_json
source: bam_readgroup_to_json/OUTPUT
out:
- id: output
- id: decider_readgroup_se
run: ../../tools/decider_readgroup_expression.cwl
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq_s
- id: readgroup_json
source: bam_readgroup_to_json/OUTPUT
out:
- id: output
- id: decider_readgroup_o1
run: ../../tools/decider_readgroup_expression.cwl
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq_o1
- id: readgroup_json
source: bam_readgroup_to_json/OUTPUT
out:
- id: output
- id: decider_readgroup_o2
run: ../../tools/decider_readgroup_expression.cwl
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq_o2
- id: readgroup_json
source: bam_readgroup_to_json/OUTPUT
out:
- id: output
- id: readgroup_fastq_pe
run: readgroup_fastq_pe.cwl
scatter: [forward_fastq, reverse_fastq, readgroup_json]
scatterMethod: "dotproduct"
in:
- id: forward_fastq
source: biobambam_bamtofastq/output_fastq1
- id: reverse_fastq
source: biobambam_bamtofastq/output_fastq2
- id: readgroup_json
source: decider_readgroup_pe/output
# - id: readgroup_meta_list
# source: readgroups_bam_file
# valueFrom: $(self.readgroup_meta_list)
out:
- id: output
- id: readgroup_fastq_se
run: readgroup_fastq_se.cwl
scatter: [fastq, readgroup_json]
scatterMethod: "dotproduct"
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq_s
- id: readgroup_json
source: decider_readgroup_se/output
# - id: readgroup_meta_list
# source: readgroups_bam_file
# valueFrom: $(self.readgroup_meta_list)
out:
- id: output
- id: readgroup_fastq_o1
run: readgroup_fastq_se.cwl
scatter: [fastq, readgroup_json]
scatterMethod: "dotproduct"
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq_o1
- id: readgroup_json
source: decider_readgroup_o1/output
# - id: readgroup_meta_list
# source: readgroups_bam_file
# valueFrom: $(self.readgroup_meta_list)
out:
- id: output
- id: readgroup_fastq_o2
run: readgroup_fastq_se.cwl
scatter: [fastq, readgroup_json]
scatterMethod: "dotproduct"
in:
- id: fastq
source: biobambam_bamtofastq/output_fastq_o2
- id: readgroup_json
source: decider_readgroup_o2/output
# - id: readgroup_meta_list
# source: readgroups_bam_file
# valueFrom: $(self.readgroup_meta_list)
out:
- id: output